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Landscape and m6A post-transcriptional regulation of soybean proteome.

Qing Yang·Zhi-Yang Hou·Linxia Li·Leili Wang·Shang-Tong Li·Yaping Li·Xuemin Zhang·Huanwei Huang·Yunzhuo Ke·Xiaofei Ma·Zexuan Wu·Zhi Liu·Xiaolei Shi·Chaofan Liu·Chen Meng·Hai Du·Mingxun Chen·Xiaofeng Gu·Zhe Yan·Faming Wang·Xiao Luo·Long Yan·Zhe Liang
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Abstract

The soybean is a critical source of vegetable protein, but its proteome remains undercharacterized. Here, we quantify 12,855 proteins across 14 soybean organs using 4D data-independent acquisition mass spectrometry (4D-DIA-MS), creating the most extensive soybean proteome dataset to date. Organ-specific protein expression and co-expression analyses highlight functional specificity with significant differences in protein-transcript abundance across organs. We also map N6-methyladenosine (m6A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of the proteome and m6A methylome identifies a novel regulator in m6A methylation. This comprehensive proteomic and m6A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement.

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Glycine maxProteomeAdenosineGene Expression Regulation, PlantPlant ProteinsProteomicsMethylationRNA Processing, Post-TranscriptionalN(6)-methyladenosineRNA methylationm(6)Amass spectrometryproteomesoybeanJournal ArticleResearch Support, Non-U.S. Gov't

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Qing Yang, Zhi-Yang Hou, Linxia Li, Leili Wang, Shang-Tong Li, Yaping Li, Xuemin Zhang, Huanwei Huang, Yunzhuo Ke, Xiaofei Ma, Zexuan Wu, Zhi Liu, Xiaolei Shi, Chaofan Liu, Chen Meng, Hai Du, Mingxun Chen, Xiaofeng Gu, Zhe Yan, Faming Wang, Xiao Luo, Long Yan, Zhe Liang. 2025-07-07. Landscape and m6A post-transcriptional regulation of soybean proteome.. https://doi.org/10.1016/j.xgen.2025.100926

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